Inflammation and premature aging in advanced chronic kidney disease

Systemic inflammation in end-stage renal disease (ESRD) is an established risk factor for mortality and a catalyst for other complications which are related to a premature aging phenotype, including muscle wasting, vascular calcification and other forms of premature vascular disease, depression, osteoporosis and frailty. Uremic inflammation is also mechanistically related to mechanisms involved in the aging process, such as telomere shortening, mitochondrial dysfunction, and altered nutrient sensing, which can have direct effect on cellular and tissue function. In addition to uremia-specific causes such as abnormalities in the phosphate- Klotho axis, there are remarkable similarities between the pathophysiology of uremic inflammation and so-called "inflammaging" in the general population. Potentially relevant, but still somewhat unexplored in this respect are abnormal or misplaced protein structures as well as abnormalities in tissue homeostasis, which evoke danger signals through damage associated molecular patters (DAMPS) as well as the senescence associated secretory phenotype (SASP). Systemic inflammation, in combination with the loss of kidney function, can impair the resilience of the body to external and internal stressors by reduced functional and structural tissue reserve, and by impairing normal organ crosstalk, thus providing an explanation for the greatly increased risk of homeostatic breakdown in this population. In this review, the relation between uremic inflammation and a premature aging phenotype, as well as potential causes and consequences are discussed

Correcting errors in synthetic DNA through consensus shuffling

Although efficient methods exist to assemble synthetic oligonucleotides into genes and genomes, these suffer from the presence of 1–3 random errors/kb of DNA. Here, we introduce a new method termed consensus shuffling and demonstrate its use to significantly reduce random errors in synthetic DNA. In this method, errors are revealed as mismatches by re-hybridization of the population. The DNA is fragmented, and mismatched fragments are removed upon binding to an immobilized mismatch binding protein (MutS). PCR assembly of the remaining fragments yields a new population of full-length sequences enriched for the consensus sequence of the input population. We show that two iterations of consensus shuffling improved a population of synthetic green fluorescent protein (GFPuv) clones from ∼60 to >90% fluorescent, and decreased errors 3.5- to 4.3-fold to final values of ∼1 error per 3500 bp. In addition, two iterations of consensus shuffling corrected a population of GFPuv clones where all members were non-functional, to a population where 82% of clones were fluorescent. Consensus shuffling should facilitate the rapid and accurate synthesis of long DNA sequences

Evaluating Within-Person Change In Implicit Measures Of Alcohol Associations: Increases In Alcohol Associations Predict Increases In Drinking Risk And Vice Versa

Aims: Implicit measures of alcohol associations (i.e. measures designed to assess associations that are fast/reflexive/impulsive) have received substantial research attention. Alcohol associations related to the self (drinking identity), the effects of alcohol (alcohol excite) and appetitive inclinations (alcohol approach) have been found to predict drinking cross-sectionally and over time. A critical next step in this line of research and the goal of this study is to evaluate whether increases in the strength of these associations predict increases in drinking and vice versa. These hypotheses were tested in a sample of first- and second-year US university students: a sample selected because this time period is associated with initiation and escalation of drinking, peak levels of alcohol consumption and severe alcohol-related negative consequences. Short summary: This study's purpose was to evaluate whether increases in the strength of alcohol associations with the self (drinking identity), excitement (alcohol excite) and approach (alcohol approach) as assessed by implicit measures predicted subsequent increases in drinking risk and vice versa using a longitudinal, university student sample. Results were consistent with hypotheses. Methods: A sample of 506 students' (57% women) alcohol associations and alcohol consumption were assessed every 3 months over a 2-year period. Participants' consumption was converted to risk categories based on NIAAA's criteria: non-drinkers, low-risk drinkers and high-risk drinkers. A series of cross-lagged panel models tested whether changes in alcohol associations predicted subsequent change in drinking risk (and vice versa). Results: Across all three measures of alcohol associations, increases in the strength of alcohol associations were associated with subsequent increases in drinking risk and vice versa. Conclusion: Results from this study indicate bi-directional relationships between increases in alcohol associations (drinking identity, alcohol excite and alcohol approach) and subsequent increases in drinking risk. Intervention and prevention efforts may benefit from targeting these associations

Mood selectively moderates the implicit alcohol association-drinking relation in college student heavy episodic drinkers

Multiple studies indicate that implicit alcohol-related associations (i.e., indices of relatively fast, spontaneous processes) predict drinking. An important next step is to investigate moderators of the implicit association-drinking relationship. Mood state has been proposed as a moderator of this relationship: implicit associations have been theorized to be stronger predictors of drinking under positive mood states. From the same theoretical perspective, explicit measures (indices of relatively slow, reflective processes) have been proposed to be stronger predictors of drinking under negative mood states. The current study evaluated these hypotheses by investigating whether mood state (manipulated via exposure to a brief video clip) moderated the relations between three types of implicit alcohol-related associations (alcohol excite, alcohol approach, and drinking identity), their explicit counterparts, and drinking in a taste test that included beer and soft drinks. A sample of 152 undergraduate social drinkers (81 men; 71 women) completed baseline measures of implicit alcohol-related associations, their explicit counterparts, and typical drinking behaviors. Participants then viewed a mood-state-inducing video clip (positive, neutral, or negative), and completed the taste test. Results were mixed but generally indicated that prediction of drinking by baseline implicit alcohol excite (but not alcohol approach or drinking identity) associations was moderated by mood. Specifically, implicit alcohol excite associations were more negatively associated with drinking after viewing the sad video and more positively associated with drinking after watching the happy/neutral video. Moderation was also observed for the explicit counterpart of alcohol excite. Findings are discussed in terms of models of negative reinforcement drinking

Small RNA profiling of low biomass samples: identification and removal of contaminants

Background Sequencing-based analyses of low-biomass samples are known to be prone to misinterpretation due to the potential presence of contaminating molecules derived from laboratory reagents and environments. DNA contamination has been previously reported, yet contamination with RNA is usually considered to be very unlikely due to its inherent instability. Small RNAs (sRNAs) identified in tissues and bodily fluids, such as blood plasma, have implications for physiology and pathology, and therefore the potential to act as disease biomarkers. Thus, the possibility for RNA contaminants demands careful evaluation. Results Herein, we report on the presence of small RNA (sRNA) contaminants in widely used microRNA extraction kits and propose an approach for their depletion. We sequenced sRNAs extracted from human plasma samples and detected important levels of non-human (exogenous) sequences whose source could be traced to the microRNA extraction columns through a careful qPCR-based analysis of several laboratory reagents. Furthermore, we also detected the presence of artefactual sequences related to these contaminants in a range of published datasets, thereby arguing in particular for a re-evaluation of reports suggesting the presence of exogenous RNAs of microbial and dietary origin in blood plasma. To avoid artefacts in future experiments, we also devise several protocols for the removal of contaminant RNAs, define minimal amounts of starting material for artefact-free analyses, and confirm the reduction of contaminant levels for identification of bona fide sequences using ‘ultra-clean’ extraction kits. Conclusion This is the first report on the presence of RNA molecules as contaminants in RNA extraction kits. The described protocols should be applied in the future to avoid confounding sRNA studies. Keywords: RNA sequencing; Artefact removal; Exogenous RNA in human blood plasma; Contaminant RNA; Spin column

Gastrointestinal symptoms, inflammation and hypoalbuminemia in chronic kidney disease patients: a cross-sectional study

BACKGROUND: Few studies have focused on investigating hypoalbuminemia in patients during earlier stages of chronic kidney disease (CKD). In particular, little is known about the role of gastrointestinal (GI) symptoms. Our goal in this paper is to study how GI symptoms relate to serum albumin levels in CKD, especially in the context of and compared with inflammation. METHODS: We performed a cross-sectional study of 3599 patients with chronic kidney disease enrolled in the Chronic Renal Insufficiency Cohort (CRIC) study. All subjects were asked to complete the Modification of Diet in Renal Disease (MDRD) study patient symptom form. Our main predictor is GI symptom score. Serum level of C-reactive protein (CRP) was measured as well. Main outcome measures are serum albumin levels and prevalence of hypoalbuminemia. RESULTS: Of the participants assessed, mean serum albumin was 3.95 ± 0.46 g/dL; 12.7 % had hypoalbuminemia. Patients with lower estimated glomerular filtration rate (eGFR) were likely to have more GI symptoms (apparent at an eGFR <45 ml/min/1.73 m(2)). Patients with worse GI symptoms had lower dietary protein intake. GI symptoms, like inflammation, were risk factors for lower serum albumin levels. However, adding GI symptom score or CRP into the multivariable regression analysis, did not attenuate the association between lower eGFR and lower albumin or hypoalbuminemia. CONCLUSIONS: Increased prevalence of GI symptoms become apparent among CKD patients at relatively high eGFR levels (45 ml/min/1.73 m(2)), long before ESRD. Patients with more severe GI symptoms scores are more likely to have hypoalbuminemia. But our data do not support GI symptoms/decreased protein intake or inflammation as being the main determinants of serum albumin level in CKD patients. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12882-015-0209-z) contains supplementary material, which is available to authorized users

The effect of postexercise carbohydrate and protein ingestion on bone metabolism

Purpose To investigate the effect of feeding carbohydrate and protein (CHO+PRO), immediately or 2 h after an exhaustive run, on the bone turnover response in endurance runners. Methods 10 men (age 28±5 y, height 1.74±0.05 m, body mass 69.7±6.3 kg) performed treadmill running at 75%VO2max, until exhaustion, on three occasions. Blood was collected before and immediately, 1, 2, 3, 4 and 24 h post-exercise, for measurement of β-CTX, P1NP, PTH, PO4, ACa and Ca2+. This was a randomised, counterbalanced, placebo-controlled, single-blinded, cross-over study. The three trials were; i) placebo (PLA), PLA solution was ingested immediately and 2 h post-exercise, ii) immediate feeding (IF), CHO+PRO (1.5 g.kgBM-1 dextrose and 0.5 g.kgBM-1 whey) were ingested immediately post-exercise and PLA 2 h post-exercise, and iii) delayed feeding (DF), PLA was ingested immediately post-exercise and CHO+PRO solution 2 h post-exercise. Data were analysed using repeated measures ANOVA and post-hoc Tukey’s HSD. Results At 1 and 2 h post-exercise, β-CTX concentrations were lower in the IF trial than the DF and PLA trials (P≤0.001). At 3 h post-exercise, β-CTX concentrations were higher in the PLA trial than the IF (P≤0.001) and DF trials (P=0.026). At 4 h post-exercise, β-CTX concentrations were lower in the DF trial than the IF (P=0.003) and PLA trials (P≤0.001). At 4 h post-exercise, P1NP was higher in the IF trial than in DF (P=0.026) and PLA trials (P=0.001). At 3 h post-exercise, PTH was higher in the IF trial than the DF trial (P≤0.001). Conclusions Following exhaustive running, immediate ingestion of CHO+PRO may be beneficial, as it decreases bone resorption marker concentrations and increases bone formation marker concentrations; creating a more positive bone turnover balance